I can access this this key using gconf-editor. However when I cd to ~/.gconf/apps/metacity I find an empty file named %gconf.xml and a directory called general which contanains another %conf.xml file which is like this:

1 Answer
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~/.gconf subfolders contain only the settings that were modified by the user. Original gconf settings can be found in /usr/share/gconf/. For example, the key /apps/metacity/global_keybindings/ you mentioned in your question is created using /usr/share/gconf/schemas/metacity.schemas. And when the user changes some settings in this key, they go to ~/.gconf/apps/metacity/global_keybindings/%gconf.xml.

BTW, gconf is superseded by dconf. Though some settings weren't transferred yet.